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First, get rid of the nesting materials altogether. Guinea pigs don't nest, and as you've found, it's dangerous. It would be even worse if he'd eaten it.
You need to clean his sac and penis sheath. See https://www.guineapigcages.com/forum/threads/85830-Awesome-video-on-how-to-clean-the-Anal-Sac for how to do it.